Centromere evolution and CpG methylation during vertebrate speciation
暂无分享,去创建一个
Koichiro Doi | Hiroyuki Takeda | Kazuki Ichikawa | S. Morishita | H. Takeda | Ryohei Nakamura | M. Kumagai | J. Yoshimura | K. Doi | Yuta Suzuki | Kazuki Ichikawa | Naoki Irie | Yui Uchida | Shingo Tomioka | Yusuke Inoue | Naoki Irie | Yusuke Inoue | Shingo Tomioka | Yuta Suzuki | Ryohei Nakamura | Jun Yoshimura | Masahiko Kumagai | Yui Uchida | Shinich Morishita | Yusuke Inoue
[1] Eugene W. Myers,et al. The fragment assembly string graph , 2005, ECCB/JBI.
[2] Jianzhi Zhang. Evolution of DMY, a newly emergent male sex-determination gene of medaka fish. , 2004, Genetics.
[3] Mark Yandell,et al. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects , 2011, BMC Bioinformatics.
[4] Taro L. Saito,et al. Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns , 2012, Genome research.
[5] I. Cheeseman,et al. The molecular basis for centromere identity and function , 2015, Nature Reviews Molecular Cell Biology.
[6] A. Shimada,et al. Occurrence of a short variant of the Tol2 transposable element in natural populations of the medaka fish. , 2011, Genetics research.
[7] F. Chen. Effects of A:T base pairs on the B-Z conformational transitions of DNA. , 1988, Nucleic acids research.
[8] N. Ogonuki,et al. Centromeric DNA hypomethylation as an epigenetic signature discriminates between germ and somatic cell lineages. , 2007, Developmental biology.
[9] Sofia M. C. Robb,et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.
[10] Michael A. Beer,et al. Discriminative prediction of mammalian enhancers from DNA sequence. , 2011, Genome research.
[11] H. Ohashi,et al. Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes , 2013, Nucleic acids research.
[12] Felix Krueger,et al. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..
[13] J. Landolin,et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing , 2014, Nature Biotechnology.
[14] Jeffrey Ross-Ibarra,et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution , 2012, Genome Biology.
[15] Kazuki Ichikawa,et al. Landscape of CpG methylation of individual repetitive elements , 2015 .
[16] Haibao Tang,et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum , 2015, Nature.
[17] Minoru Tanaka,et al. Medaka : a model for organogenesis, human disease, and evolution , 2011 .
[18] Dmitry Pushkarev,et al. Whole-genome haplotyping using long reads and statistical methods , 2014, Nature Biotechnology.
[19] G. P. Smith,et al. Evolution of repeated DNA sequences by unequal crossover. , 1976, Science.
[20] Jiming Jiang,et al. Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome. , 2011, Genome research.
[21] Gabor T. Marth,et al. An integrated map of structural variation in 2,504 human genomes , 2015, Nature.
[22] Bradley P. Coe,et al. Genome structural variation discovery and genotyping , 2011, Nature Reviews Genetics.
[23] Eugene W. Myers,et al. Efficient Local Alignment Discovery amongst Noisy Long Reads , 2014, WABI.
[24] Y. Bessho,et al. Transposable element in fish , 1996, Nature.
[25] Stephen C. J. Parker,et al. DNA sequence and analysis of human chromosome 8 , 2006, Nature.
[26] M. Borodovsky,et al. Gene identification in novel eukaryotic genomes by self-training algorithm , 2005, Nucleic acids research.
[27] Jonas Korlach,et al. Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures , 2008, Proceedings of the National Academy of Sciences.
[28] Fumiko Ohta,et al. The medaka draft genome and insights into vertebrate genome evolution , 2007, Nature.
[29] Ulrich Bodenhofer,et al. KeBABS: an R package for kernel-based analysis of biological sequences , 2015, Bioinform..
[30] Ian Korf,et al. Gene finding in novel genomes , 2004, BMC Bioinformatics.
[31] Shuichi Asakawa,et al. DMY is a Y-specific DM-domain gene required for male development in the medaka fish , 2002, Nature.
[32] S. Turner,et al. Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.
[33] I. Dunham,et al. DNA sequence and analysis of human chromosome 9 , 2003, Nature.
[34] S. Neuhauss,et al. Whole-genome duplication in teleost fishes and its evolutionary consequences , 2014, Molecular Genetics and Genomics.
[35] Aaron A. Klammer,et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.
[36] Ali Bashir,et al. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing , 2016, Bioinform..
[37] S. Turner,et al. Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations , 2003, Science.
[38] Christina A. Cuomo,et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.
[39] M. Schartl,et al. Genomic organization of the sex-determining and adjacent regions of the sex chromosomes of medaka. , 2006, Genome research.
[40] Ewan Birney,et al. Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish , 2014, G3: Genes, Genomes, Genetics.
[41] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[42] Mark J. P. Chaisson,et al. Resolving the complexity of the human genome using single-molecule sequencing , 2014, Nature.
[43] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[44] Mihai Pop,et al. DNACLUST: accurate and efficient clustering of phylogenetic marker genes , 2011, BMC Bioinformatics.
[45] N. Nagai,et al. Geographic Variation and Diversity of the Cytochrome b Gene in Japanese Wild Populations of Medaka, Oryzias latipes , 2003, Zoological science.
[46] David L. Steffen,et al. The DNA sequence of the human X chromosome , 2005, Nature.
[47] David Haussler,et al. Long-read sequence assembly of the gorilla genome , 2016, Science.
[48] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[49] Alan Christoffels,et al. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding , 2016, PLoS genetics.
[50] Huntington F. Willard,et al. Hierarchical order in chromosome-specific human alpha satellite DNA , 1987 .
[51] D. Chalopin,et al. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates , 2015, Chromosome Research.
[52] H. Inoko,et al. Genetic linkage map of medaka with polymerase chain reaction length polymorphisms. , 2005, Gene.
[53] S. Henikoff,et al. The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA , 2001, Science.
[54] S. V. van Heeringen,et al. Principles of nucleation of H3K27 methylation during embryonic development , 2014, Genome research.
[55] S. Sugano,et al. Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species , 2015, BMC Genomics.
[56] Keith Bradnam,et al. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..
[57] Hiroyuki Takeda,et al. The art of medaka genetics and genomics: what makes them so unique? , 2010, Annual review of genetics.
[58] A. Shimada,et al. Evidence for recent invasion of the medaka fish genome by the Tol2 transposable element. , 2000, Genetics.
[59] C. White,et al. Centromere Associations in Meiotic Chromosome Pairing. , 2015, Annual review of genetics.
[60] Russell E. Durrett,et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies , 2015, Nature Methods.
[61] Y. Kuwahara,et al. γ‐Ray exposure accelerates spermatogenesis of medaka fish, Oryzias latipes , 2003 .
[62] F. Chen,et al. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. , 2010, The Plant journal : for cell and molecular biology.
[63] T Aida,et al. On the Inheritance of Color in a Fresh-Water Fish, APLOCHEILUS LATIPES Temmick and Schlegel, with Special Reference to Sex-Linked Inheritance. , 1921, Genetics.
[64] Eleazar Eskin,et al. The Spectrum Kernel: A String Kernel for SVM Protein Classification , 2001, Pacific Symposium on Biocomputing.
[65] E. Winzeler,et al. Genomic and Genetic Definition of a Functional Human Centromere , 2001, Science.
[66] G. Karpen,et al. Epigenetic regulation of centromeric chromatin: old dogs, new tricks? , 2008, Nature Reviews Genetics.
[67] Taro L. Saito,et al. Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates , 2014, Development.
[68] C. Feschotte. Transposable elements and the evolution of regulatory networks , 2008, Nature Reviews Genetics.
[69] M. Schatz,et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.
[70] J. Inoue,et al. Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates , 2009, Biology Letters.
[71] Nicolas Altemose,et al. Centromere reference models for human chromosomes X and Y satellite arrays , 2013, Genome research.
[72] I. Longden,et al. EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.
[73] Valery Shepelev,et al. Alpha-satellite DNA of primates: old and new families , 2001, Chromosoma.